Hi Sita,
Thanks for your reply.
A follow up question I have and that is so how about measurements in
mris_anatomical_stats? Wouldn't total WM volume be affected by an
inaccurate wm.mgz or does freesurfer use surfaces to compute the
volumes?
Thank you,
Nasim
On Mar 3, 2009, at 6:26 PM,
Nick,
I confess, I am not exactly sure what you mean by "turn off annotation
display". I tried a few things.
- If I don't include the -annot option in tksurfer it only displays the
fsaverage, naturally.
- If I toggle off the button that says "show labels", it looks like it is
just
Hello,
I am not sure what y-axis values are in a time course plot.
Here is my bugr information:
FREESURFER_HOME: /usr/local/freesurfer/stable4
Build stamp: freesurfer-Linux-centos4-stable-v4.2.0d-20090227
RedHat release: CentOS release 5.2 (Final)
Kernel info: Linux 2.6.18-92.el5 i686
NMR Ce
The time courses are independent of the contrasts. The time course
values are the MR units globally scaled to a grand mean of 1000, so you
can think of the units as 10ths of percent. I think you can configure
the time course to show vertex-by-vertex percentages.
doug
Dave Brohawn wrote:
Hell
Dear Freesurfer community:
Postdoctoral positions are available in the Jagust Lab in the Helen
Wills Neuroscience Institute at the University of California,
Berkeley. We are studying brain aging using PET, structural MRI and
fMRI. One project uses PET to measure brain beta-amyloid accumulation
wi
If you use mris_wm_volume, it will compute the volume enclosed by the
$h.white surfaces. It's more accurate than using mris_anatomical_stats
for white matter. I believe you don't need to edit wm.mgz, assuming the
$h.white surfaces accurately follow the white matter in your images.
Nasim Maleki
Dear all,
I've come across a similar problem to the one described before in qdec,
but cannot find a solution for it,
I've previously visualised my data using qdec, but when I tried to run
it again I get the following error. I've checked to make sure my subject
is named correctly and I am in the
Prapti,
Try deleting the directory 'qdec/Untitled' and run it again. Prior to
v4.2.0, qdec did not delete that directory, which is the default working
directory, so its possible some incompatible files from a prior run were
lingering.
Nick
On Thu, 2009-03-05 at 09:42 +1100, Prapti Gautam wrote
Deleting 'qdec/Untitled' worked! Thanks,
Prapti
-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: Thursday, 5 March 2009 11:10 AM
To: Prapti Gautam
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] qdec error in analyze
Prapti,
Try deleting the dire
Good. I forgot to mention, the 'Design Name' entry box on the Design
tab is intended for keep track of a particular analysis. For instance
lets say your looking at thickness on the left hemi where you have
selected diagnosis and age as factors. You might want to name the
Design 'diagnosis_age_th
Hi all,
In recon-all pipeline , mri_segstats runs with -pv mri/norm.mgz
option ,as written from
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats , it is used to
compensate partial voluming. I wonder what exactly does this do, as the volumes
given by aseg.stats are different from
aseg.mgz a
Hi Anthony,
it should be more accurate (and more reliable in our studies). It
estimates the volume fraction of each tissue class on the border of the
structure, assuming it is mixed with adjacent classes by estimating the
local mean of the two tissue classes, then computing the mixing
coeffic
Hi Bruce,
Thanks a lot for your reply . Is there anyway that I can get a mask for a
certain class (e.g WM) after partial volume correction using FS ? Or is it
possible for you to provide more details of it so I can reproduce the
calculation to get the mask ?
Anthony
--- On Thu, 5/3/09, Bruce
Hi all. Documentation estimates 30 minutes for -autorecon1 on the
sample data provided with the most recent freesurfer release. Our 2008
iMac with 4GB of RAM takes about 90 minutes. Throughout the job CPU
utilization was high but there was plenty of free RAM.
Is 90 minutes common for similarly equ
Hi Anthony,
we're happy to provide the code, but there's no easy way to get a mask,
since each border voxel has more than 1 label in it.
cheers,
Bruce
On Wed, 4 Mar 2009, Anthony wrote:
Hi Bruce,
Thanks a lot for your reply . Is there anyway that I can get a mask for a
certain class (e.g
Stephen,
The 30 minute estimate for the -autorecon1 stage is no longer accurate.
It got slower when we added a feature to improved the skull-strip step.
The feature is to make use of an atlas to determine where skull and
cerebellum might be. To use that atlas requires a registration to that
atlas
Hi Bruce,
That would be great. I'm aware of the difficulty in putting partial volume
information into segmentation, but maybe it could help to achieve other useful
information as aseg.stats only provides the total volume for each label.
Thanks,
Anthony
--- On Thu, 5/3/09, Bruce Fischl wrote:
sure, you're welcome to a beta of the source distribution.
cheers,
Bruce
On Wed, 4 Mar
2009, Anthony wrote:
Hi Bruce,
That would be great. I'm aware of the difficulty in putting partial volume
information into segmentation, but maybe it could help to achieve other useful
information as ase
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